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Sample GSM866081 Query DataSets for GSM866081
Status Public on Aug 01, 2012
Title Splenic Marginal Zone Lymphoma P21 50XbaI
Sample type genomic
 
Source name Splenic Marginal Zone Lymphoma P21
Organism Homo sapiens
Characteristics tissue: Splenic Marginal Zone Lymphoma
Treatment protocol Not treatment
Growth protocol Cells were cultured in RPMI-1640 medium supplemented with 10% FBS
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from mononuclear cells and cell lines using the Qiagen DNA Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.
Label Biotin
Label protocol As per manufacturer (Affymetrix)
 
Hybridization protocol DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
Scan protocol The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
Description Hybridized to 50K_Xba
Data processing The CEL files were analyzed using the aroma.affymetrix package of R/Bioconductor (CRLMM-algorithm to produce genotype calls and SNPRMA to produce the summarized signal).
 
Submission date Jan 25, 2012
Last update date Aug 01, 2012
Contact name Vicente Jose Fresquet
E-mail(s) vfresquet@unav.es
Phone 34-948-194700
Fax 34-948-194714
Organization name Center for Applied Medical Research (Cima)
Department Division of Oncology
Lab Molecular Oncology
Street address Av Pio XII 55
City Pamplona
State/province Navarra
ZIP/Postal code 31008
Country Spain
 
Platform ID GPL2005
Series (2)
GSE35329 INTEGRATIVE ONCOGENOMIC AND HIGH-THROUGHPUT SEQUENCING ANALYSES OF THE COMMONLY DELETED REGION IN CHROMOSOME 7q32 IN SPLENIC MARGINAL ZONE LYMPHOMA (SNP data)
GSE35383 INTEGRATIVE ONCOGENOMIC AND HIGH-THROUGHPUT SEQUENCING ANALYSES OF THE COMMONLY DELETED REGION IN CHROMOSOME 7q32 IN SPLENIC MARGINAL ZONE LYMPHOMA

Data table header descriptions
ID_REF
VALUE Genotype Call (SNP call): AA, AB, BB; 'Signal' = Summarized signal
Xba_SIGNAL

Data table
ID_REF VALUE Xba_SIGNAL
SNP_A-1507972 AB 28758.05615
SNP_A-1510136 BB 10587.99872
SNP_A-1511055 BB 21937.10181
SNP_A-1518245 BB 17115.15912
SNP_A-1641749 BB 14877.30396
SNP_A-1641751 AB 25028.24463
SNP_A-1641753 AB 27765.0835
SNP_A-1641755 AA 29214.30994
SNP_A-1641757 AB 25422.98389
SNP_A-1641759 AB 26517.98584
SNP_A-1641761 AB 25412.67285
SNP_A-1641763 AB 20799.40991
SNP_A-1641765 AA 7968.137054
SNP_A-1641767 AA 20525.07306
SNP_A-1641769 BB 38432.73218
SNP_A-1641771 BB 9535.347534
SNP_A-1641773 BB 19428.40259
SNP_A-1641775 AB 19369.3999
SNP_A-1641777 AB 30786.04443
SNP_A-1641779 BB 9073.275146

Total number of rows: 58960

Table truncated, full table size 1663 Kbytes.




Supplementary file Size Download File type/resource
GSM866081.CEL.gz 14.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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